Wang Lab @ Biostatistics Department

Softwares

Sigma-P Method for Rare-Variant Analysis

SigmaP is a rare-variant method for detecting disease associations
in case-control sequencing studies. The Sigma-P statistic aggregates the effects of multiple variant
sites by computing a weighted sum of the log p-values per site. Each site is weighted by the inverse
of its expected standard deviation (denoted by sigma) of the number of variants in controls.
The method is robust against signal noise introduced by a large number of neutral variants and is
effective for handling variants with opposite effects.

pclogit is an R package for penalized conditional/unconditional
logistic regression using a network-based peanlty for matched/unmatched case-control data
with grouped or graph-constrained variables. The algorithm is efficient for fitting the
regularization path and for providing selection probabilities of each predictor for the
anaylsis of high-dimensional matched/unmatched case-control data. It uses cyclical
coordinate descent in a pathwise fashion.

Rare variants selection - rvsel R package

rvsel is an R package for rare variants selection with sequence data.
The most outome-related rare variants are selected within a gene or a genetic region.
The selection procedure is based on the power set of the subset of the rare variants.

NEpiC: a Network-assisted algorithm for Epigenetic studies using mean and variance Combined signals

We present a network-assisted algorithm, NEpiC, that combines both mean and variance signals in searching for differentially methylated sub-networks using the protein-protein interaction (PPI) network.

Most existing methods developed to identify differentially methylated loci (DML) use mean signals only, and only a few methods were developed to identify DML using both mean and variance signals, while all existing methods to detect differentially methylated regions (DMRs) focus on mean signals only. This R code is for the new DMR detection algorithm we proposed that uses mean and variance combined signals.

To estimate the number of cell divisions (mitotic age) of a given tissue type between individuals is of great interest as that allows their stratification of prospective cancer risk. Here we introduce the MiAge Calculator, a DNA methylation-based mitotic clock calculator based on a novel statistical method MiAge, designed to quantitatively estimate mitotic age of a tissue of an individual. This R code is for the new DMR detection algorithm we proposed that uses mean and variance combined signals.